Update:
New changes to sections 3.3.1, 3.3.2 and 3.3.9 have made MonoTouch (and all other cross compilers/languages/etc) perfectly acceptable on the iPhone. See Apple's announcement
Miguel doesn't seem to think so. See the tweet and Miguel's response. Lets not overreact here and say that Monotouch is dead, or stop developing with Monotouch until some clarifications have been made by all parties involved.
That said I would definitely start putting the heat on Apple for such draconian development policies. Things like this, and the nebulous process that is the approval policy of iphone/ipad/touch apps should strike fear into the hearts of developers. What's next, their license stating that the only Ad platform you are allowed to use is iAd? Not allowing the distribution of free apps without iAd? Slowly raising Apple's share of the revenue of app sales? As developers in a locked down eco-system, we are kind of frogs in a pot of hot water, and Apple is slowly turning up the heat. Now is the time to explore other mobile platforms, because as they get better, the main thing holding people to the Apple platform is lack of applications on other platforms.